crossing96/oncoscreening huggingface dataset:
Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications.	BACKGROUND: Integrated molecular profiling has identified intrinsic expression-based bladder cancer molecular subtypes. Despite frequent histological diversity, robustness of subtypes in paired conventional (urothelial) and squamous components of the same bladder tumor has not been reported. OBJECTIVE: To assess the impact of histological heterogeneity on expression-based bladder cancer subtypes. DESIGN, SETTING, AND PARTICIPANTS: We performed clinically applicable, targeted DNA and/or RNA sequencing (multiplexed DNA and RNA sequencing [mxDNAseq and mxRNAseq, respectively]) on 112 formalin-fixed paraffin-embedded (FFPE) bladder cancer samples, including 12 cases with paired urothelial/squamous components and 21 bladder cancer cell lines. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Unsupervised hierarchical and consensus clustering of target gene expression enabled derivation of basal/luminal molecular subtyping. RESULTS AND LIMITATION: Across 21 bladder cancer cell lines, our custom mxRNAseq panel was highly concordant with whole transcriptome sequencing, and assessed targets robustly determined expression-based basal/luminal subtypes from The Cancer Genome Atlas data (in silico) and internally sequenced FFPE tissues. Frequent deleterious TP53 (56%) and activating hotspot PIK3CA (30%) somatic mutations were seen across 69 high-quality tissue samples. Potentially targetable focal ERBB2 (6%) or EGFR (6%) amplifications were also identified, and a novel subgene copy-number detection approach is described. Combined DNA/RNA analysis showed that focally amplified samples exhibit outlier EGFR and ERBB2 expression distinct from subtype-intrinsic profiles. Critically, paired urothelial and squamous components showed divergent basal/luminal status in three of 12 cases (25%), despite identical putatively clonal prioritized somatic genomic alterations. Limitations include lack of profiled paired normal tissues for formal somatic alteration determination, and the need for formal analytical and clinical validation. CONCLUSIONS: Our results support the feasibility of clinically relevant integrative bladder cancer profiling and challenge the intrinsic nature of expression subtypes in histologically diverse bladder cancers. PATIENT SUMMARY: A targeted RNA sequencing assay is capable of assessing gene expression-based subtypes in individual components of clinical bladder cancer tissue specimens. Different histological components of the same tumor may yield divergent expression profiles, suggesting that expression-based subtypes should be interpreted with caution in heterogeneous cancers.	bladder
Correlation between malnutrition, body mass index and complications in patients with urinary bladder cancer who underwent radical cystectomy.	BACKGROUND: Nutrition is the 3rd most important factor in surgery, following anesthesia and asepsis. Until now, it has been a poorly explored field of urology. The relationship between malnutrition and postoperative complications has been proven beyond doubt in general surgery, where 30% of patients are operated in a malnutrition state. OBJECTIVES: The aim of our work was to assess the influence of malnutrition, defined by nutritional risk screening (NRS) scale and body mass index (BMI), on postoperative results in patients with bladder cancer after radical cystectomy. MATERIAL AND METHODS: The research was carried out at 8 urological centers between 2012 and 2014, and included patients with bladder cancer at stage from T2 to T4, who underwent radical cystectomy. The degree of malnutrition was assessed with the aid of the NRS 2002 questionnaire. Other examined parameters were BMI, age, type of operation, and the number of complications, the latter of which were measured by applying the Clavien-Dindo scale. RESULTS: A total of 125 patients were enrolled in our study, out of whom 64 (51.2%) were undernourished. According to the BMI, most of the patients were overweight - 50 (40%) or had normal body weight - 49 (39.2%); 24 (19.2%) were obese, and 2 (1.6%) were underweight. CONCLUSIONS: There was no relationship between malnutrition, defined by the NRS scale, and postoperative complications, and we did not find a significant relationship between the other tested variables. We observed only 1 significant relationship between the nutrition state, measured by BMI scale, and the degree in Clavien-Dindo scale. Body mass index under 18.5 and over 30 increased postoperative complications. Nowadays, the recommended scale is NRS 2002, which is based mostly on loss of weight. In our patients, qualitative malnutrition is more probable than quantitative malnutrition.	bladder
Death from Transfusion-Transmitted Anaplasmosis, New York, USA, 2017.	We report a death from transfusion-transmitted anaplasmosis in a 78-year-old man. The patient died of septic shock 2 weeks after a perioperative transfusion with erythrocytes harboring Anaplasma phagocytophilum. The patient's blood specimens were positive for A. phagocytophilum DNA beginning 7 days after transfusion; serologic testing remained negative until death.	bladder
Suppression of the SDF‑1/CXCR4/β‑catenin axis contributes to bladder cancer cell growth inhibition in vitro and in vivo.	Previous studies have found that the activation of stromal cell‑derived factor‑1 (SDF‑1)/CXC chemokine receptor‑4 (CXCR4)/β‑catenin signaling is associated with biological malignant potential in cancers. However, its function has been rarely reported in the progression of bladder cancer (BCa). The aim of the present study was to investigate the association of SDF‑1/CXCR4 signaling and β‑catenin in regards to BCa cell proliferation, colony formation, migration and invasion. The methods used were MTS, colony formation, and Transwell migration and invasion assays which were performed in SW780 cells following treatment with the CXCR4 antagonist AMD3465, SDF‑1, the β‑catenin antagonist FH535, AMD3465+SDF‑1 or FH535+SDF‑1. The mRNA and protein levels were assayed by RT‑qPCR and western blotting, respectively. The effect of AMD3465 on SW780 cell xenograft growth in vivo was evaluated using a nude mouse model. According to our results, human BCa SW780 cells were identified as having high expression of CXCR4 and β‑catenin. Subsequently, we found that both CXCR4 and β‑catenin antagonists could significantly inhibit the proliferation, colony formation, migration and invasion of SW780 cells. Notably, SDF‑1 could reverse the inhibitory effects of AMD3465 and FH535 on proliferation, colony formation, migration and invasion in SW780 cells. In AMD3465‑treated SW780 cells, the expression of c‑myc was significantly upregulated, and E‑cadherin was downregulated in the presence of SDF‑1. Furthermore, the tumor volume and average weight in the AMD3465‑treated group were evidently less than these parameters in the control group, indicating that AMD3465 can inhibit SW780 cell growth in vivo. In conclusion, targeting the SDF‑1/CXCR4/β‑catenin axis may be a potential therapeutic target for suppressing BCa progression.	bladder
A novel regulatory circuit of miR‑152 and DNMT1 in human bladder cancer.	Downregulation of microRNA‑152 (miR‑152) has been observed in various types of human malignancies, including Bladder cancer (BC). However, the role of miR‑152 in the development and progression of BC is still unclear. In our previous study, we identified a functional crosstalk between miR‑152 and DNA methyltransferase 1 (DNMT1) involved in Nis‑induced malignant transformation. In the present study, we found that the expression of miR‑152 was specifically downregulated in BC cells and tissues via the DNA hypermethylation of the miR‑152 promoter. The overexpression of miR‑152 in BC cells resulted in a reduction of DNMT1, whereas the inhibition of the expression of miR‑152 induced an elevated level of DNMT1. Further studies revealed that miR‑152 directly downregulated the expression of DNMT1 by targeting the 3'‑UTR of its transcript in BC cells. In addition, ectopic expression of miR‑152 in BC cells significantly inhibited cell proliferation, whereas the inhibition of miR‑152 expression led to increased cell proliferation. These findings indicated a novel regulatory circuit of miR‑152/DNMT1 in BC, and more importantly, the combination of miR‑152 and DNMT1 may function as promising therapeutic modalities and early biomarkers for BC.	bladder
The Splicing Factor PTBP1 Promotes Expression of Oncogenic Splice Variants and Predicts Poor Prognosis in Patients with Non-muscle-Invasive Bladder Cancer.	Purpose: Non-muscle-invasive bladder cancer (NMIBC) is a malignant disease characterized by high heterogeneity, which corresponds to dysregulated gene expression and alternative splicing (AS) profiles. Bioinformatics analyses of splicing factors potentially linked to bladder cancer progression identified the heterogeneous nuclear ribonucleoprotein I (i.e., PTBP1) as candidate. This study aimed at investigating whether PTBP1 expression associates with clinical outcome in patients with NMIBC.Experimental Design: A cohort of 152 patients presenting with primary NMIBC (pTa-pT1) was enrolled. Primary NMIBCs were assessed for PTBP1 expression by IHC, and the results were correlated with clinical data using Kaplan-Meier curves and Cox regression analyses. Cell proliferation and survival assays were performed to assess the function of PTBP1. Furthermore, the impact of PTBP1 on the AS pattern of specific bladder cancer-related genes was investigated in cancer cell lines and in patients' specimens.Results: Public datasets querying highlighted a positive correlation between PTBP1 expression and NMIBC progression, which was then confirmed by IHC analysis. High PTBP1 expression was associated with worse clinical outcome in terms of incidence of tumor relapse and survival in patients with NMIBC. Interestingly, downregulation of PTBP1 in bladder cancer cell lines affected prosurvival features. Accordingly, PTBP1 modulated AS of bladder cancer-related genes in cell lines and patient's specimens.Conclusions: PTBP1 expression correlates with disease progression, poor prognosis, and worse survival in patients with NMIBC. Downregulation of PTBP1 expression affects prosurvival features of bladder cancer cells and modulates AS of genes with relevance for bladder cancer, suggesting its role as an outcome-predictor in this disease. Clin Cancer Res; 24(21); 5422-32. ©2018 AACR.	bladder
LIMK2 acts as an oncogene in bladder cancer and its functional SNP in the microRNA-135a binding site affects bladder cancer risk.	LIM kinases modulate multiple aspects of cancer development, including cell proliferation and survival. As the mechanisms of LIMK-associated tumorigenesis are still unclear, we analyzed the tumorigenic functions of LIM kinase 2 (LIMK2) in human bladder cancer (BC) and explored whether the newly identified LIMK2 3´-UTR SNP rs2073859 (G-to-A allele) is correlated with clinical features. Expression levels of LIMK2 in 38 human BC tissues and eight cell lines were examined using quantitative real-time PCR and immunohistochemistry. LIMK2 was overexpressed in most BC tissues (27/38, 71%) and BC-derived cell lines (6/8), and was more frequently overexpessed in high-grade than low-grade BC (80% vs. 47%). The effects of LIMK2 on BC cell proliferation, survival and migration, were studied by overexpression and RNA interference approaches in vitro and in vivo. LIMK2 overexpression promoted proliferation, migration and invasion of BC cells, while LIMK2 depletion inhibited cell invasion and viability and induced growth arrest in vitro and in vivo. PCR-Restriction Fragment Length Polymorphism (RFLP) was used to genotype LIMK2 SNP rs2073859 and multivariate logistic regression applied to assess the relationship between allele frequency and clinical features in 139 BC patients. Functional analyses localized SNP rs2073859 within the microRNA-135a seed-binding region and revealed significantly lower LIMK2 G allele expression. The frequency of A genotypes (AG + AA) was higher in the BC group than normal controls and correlated with risks of high-grade and high-stage BC. In conclusion, LIMK2 may function as an oncogene in human BC, while allele-specific regulation by microRNA-135a may influence disease risk.	bladder
Electrochemical ELISA-based platform for bladder cancer protein biomarker detection in urine.	A novel fluidic-based electrochemical ELISA platform is descried for estimation of the bladder cancer protein markers nuclear mitotic apparatus protein 1 (NUMA1) and complement factor H-related 1 (CFHR1). The platform uses an off-site chamber for a sandwich immunoassay and performs the electrochemistry on-chip in a separate chamber. The off-site matrices were connected to the sensor chip in a manner that the sensors were exposed only to the final electroactive product for signal detection, thus avoiding interference from other molecules present in the sample. Two off-site matrices using 3D polymethyl methacrylate (PMMA) sheets and 2D polycarbonate (PC) membranes modified with the desired antibodies were investigated. Antibodies for NUMA1 and CFHR1 were utilized for the immunoassay and hair comb structured gold electrodes were used for sensing. Results in 10% synthetic urine reveal that the system can detect NUMA1 and CFHR1 in the 1-100 ng/ml range with high sensitivities of 260 nA/(ng/ml) and 310 nA/(ng/ml), for NUMA1 and CFHR1, respectively; negligible interference from the diluted urine and other molecules has been observed. A fully automated fluidic prototype has also been developed to demonstrate that automation of the process and multiplexing of detection can be achieved in a small footprint benchtop device. The use of off-site matrix-based platforms paves the way towards a new generation of electrochemical immunosensors for biomarker estimation with negligible non-specific interactions and false signals in complex samples.	bladder
FDG-PET/CT for Assessing the Response to Neoadjuvant Chemotherapy in Bladder Cancer Patients.	PURPOSE: To determine the accuracy of (18)F-fluorodeoxyglucose with positron emission tomography and computed tomography (FDG-PET/CT) scans in assessing the response to neoadjuvant chemotherapy (NAC) in patients with bladder cancer scheduled to undergo radical cystectomy (RC). PATIENTS AND METHODS: All patients treated at our center for muscle-invasive bladder cancer (MIBC) were counseled and offered NAC before RC. FDG-PET/CT scans were performed before the initiation of chemotherapy and after completion of the regimen. Patients with disease with complete response to NAC were those who had (pT0) or residual carcinoma-in-situ (pTis) on final pathology. Those who were downstaged from MIBC to non-MIBC were considered to have a chemosensitive tumor. We used percentage reduction in standardized maximum uptake value (SUV(max)) from PET/CT scans as our measure to correlate with the final pathology after cystectomy. RESULTS: Thirty-seven patients with MIBC who underwent NAC followed by RC were included in the final analysis. FDG-PET/CT had 75% sensitivity (89.66% specificity) in identifying those with complete pathologic response with a 100% change in SUV(max), and 83% sensitivity (94% specificity) for the detection of chemosensitive tumors. CONCLUSION: FDG-PET/CT can help determine the response of primary tumor to NAC in patients with MIBC and thus can more accurately predict the prognosis of the patients, or potentially the appropriate time for cystectomy.	bladder
Gemcitabine hydrochloride microspheres used for intravesical treatment of superficial bladder cancer: a comprehensive in vitro/ex vivo/in vivo evaluation.	INTRODUCTION: Bladder cancer is responsible for more than 130,000 deaths annually worldwide. Intravesical delivery of chemotherapeutic agents provides effective drug localization to the target area to reduce toxicity and increase efficacy. This study aimed to develop an intravesical delivery system of gemcitabine HCl (Gem-HCl) to provide a sustained-release profile, to prolong residence time, and to enhance its efficiency in the treatment of bladder cancer. MATERIALS AND METHODS: For this purpose, bioadhesive microspheres were successfully prepared with average particle size, encapsulation efficiency, and loading capacity of 98.4 µm, 82.657%±5.817%, and 12.501±0.881 mg, respectively. For intravesical administration, bioadhesive microspheres were dispersed in mucoadhesive chitosan or in situ poloxamer gels and characterized in terms of gelation temperature, viscosity, mechanical, syringeability, and bioadhesive and rheological properties. The cytotoxic effects of Gem-HCl solution, Gem-HCl microspheres, and Gem-HCl microsphere-loaded gel formulations were evaluated in two different bladder cancer cell lines: T24 (ATCC HTB4TM) and RT4 (ATCC HTB2TM). RESULTS: According to cell-culture studies, Gem-HCl microsphere-loaded poloxamer gel was more cytotoxic than Gem-HCl microsphere-loaded chitosan gel. Antitumor efficacy of newly developed formulations were investigated by in vivo studies using bladder-tumor-induced rats. CONCLUSION: According to in vivo studies, Gem-HCl microsphere-loaded poloxamer gel was found to be an effective and promising alternative for current intravesical delivery-system therapies.	bladder
Identifying a panel of genes/proteins/miRNAs modulated by arsenicals in bladder, prostate, kidney cancers.	Arsenic and arsenic-derivative compounds, named as arsenicals, represent a worldwide problem for their effect on the human health and, in particular, for their capability to increase the risk of developing cancer such as kidney, bladder and prostate cancer. The main source of arsenical exposure is drinking water. Nowadays, it is well known that the chronic exposure to arsenicals leads to a series of epigenetic alterations that have a role in arsenic-induced effects on human health including cancer. Based on these observations, the aim of our study was to select by network analysis the genes/proteins/miRNAs implicated in kidney, bladder and prostate cancer development upon arsenical exposure. From this analysis we identified: (i) the nodes linking the three molecular networks specific for kidney, bladder and prostate cancer; (ii) the relative HUB nodes (RXRA, MAP3K7, NR3C1, PABPC1, NDRG1, RELA and CTNNB1) that link the three cancer networks; (iii) the miRNAs able to target these HUB nodes. In conclusion, we highlighted a panel of potential molecules related to the molecular mechanisms of arsenical-induced cancerogenesis and suggest their utility as biomarkers or therapeutic targets.	bladder
Mesenchymal Stem Cells Promote Tumor Progression via Inducing Stroma Remodeling on Rabbit VX2 Bladder Tumor Model.	Background and aim: Mesenchymal stem cells (MSCs) are capable of impacting tumor progression but its role in tumor stroma remodeling still remains unclear. This present study was aimed to evaluate the potential function of MSCs on tumor stroma remodeling using rabbits VX2 bladder tumor model. Methods: The VX2 bladder tumor models were established by injecting mixed cell suspensions (10(6) of VX2 tumor cells and 0/10(6)/10(7) of autologous MSCs in group A, B, C, respectively) into the bladder mucosa using thirty male New Zealand white rabbits. The tumor volume was measured by ultrasound at the time points of 1st, 2nd, 3rd and 4th week after inoculation. At the end of the fourth week, the tumor tissue expressions of basic fibroblast growth factor (bFGF), transforming growth factor beta 1 (TGFβ-1), hepatocyte growth factor (HGF), matrix metalloproteinase 2 (MMP2) and matrix metalloproteinase 9 (MMP9) were determined using Real-time quantitative PCR and immunohistochemistry. Masson trichrome staining and Cy3-FITC double-labelled immunofluorescence staining were used to determine the MSCs distribution in tumor tissue in another two rabbits implanted with a cell suspension of 10(6) VX2 tumor cells and 10(6) autologous MSCs. Results: MSCs were homogeneously distributed in tumor tissues after 7 days of inoculation, which were not consistent with the distribution of tumor stroma. After 21 days of inoculation, MSCs have been integrated into tumor interstitial tissue and mainly distributed in the mesenchyma around the tumor nest. At the 1st, 2nd, 3rd and 4th week time point, tumor volume in group A < group B < group C, and the difference has statistical significance (all p<0.001).The relative mRNA and protein levels of bFGF, TGFβ-1 and HGF were significantly higher in group B and C compared with group A (all p<0.05), as well as the mRNA levels of bFGF, HGF were higher in group C than group B (p<0.05), and the protein levels of bFGF, TGFβ-1 were higher in group C than group B (p<0.05). The mRNA and protein levels of MMP2 were significantly higher in group B, C than group A (p<0.05). MMP9 was increasingly over expressed along with the growing amount of MSCs inoculated within tumor, both at the level of mRNA and protein (all p<0.05). Conclusion: MSCs participate in tumor stroma remodeling via inducing overexpression of some important growth factors and MMPs.	bladder
Pembrolizumab and epacadostat induced fatal myocarditis and myositis presenting as a case of ptosis and ophthalmoplegia.	We report the first case of fatal myocarditis presenting as bilateral ptosis in a patient on combination therapy with pembrolizumab and epacadostat. An 83 year-old man with stage III high-grade urothelial carcinoma presented with acute onset droopy eyelids one month after starting pembrolizumab and epacadostat. Exam showed myogenic ptosis and ophthalmoplegia. He was later found to have acute myocarditis with complete heart block and subsequently passed away. Pembrolizumab in combination with epacadostat can induce a potentially fatal myocarditis. Although immune mediated myocarditis is a rare established side effect, more reported fatalities are needed in the literature to highlight the urgency for standardized cardiac monitoring of even asymptomatic patients to prevent fatal outcomes, as well as a consensus on treatment protocols. Cancer immunotherapy complications are not well known to ophthalmologists. This case is unique in that the presenting sign was ptosis, which prompted the patient to call his ophthalmologist first.	bladder
[Mycotic aorta aneurysm treated with an autologous venous graft].	Systemic side effects, including sepsis, due to bacille Calmette-Guérin treatment for carcinoma in situ in the bladder, are observed in 15% of the patients. In rare cases, patients have developed systemic infections and mycotic aneurysms. In this case report, a 72-year-old man developed a mycotic aortic aneurysm, and the appropriate tuberculostatic drugs had no effect on his systemic infection. He was successfully treated surgically, replacing the affected aortic segment with an autologous venous graft, resulting in complete remission. A follow-up PET-CT three months later showed no sign of ongoing aortic infection.	bladder